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Sample GSM989786 Query DataSets for GSM989786
Status Public on Aug 23, 2012
Title PC 157N
Sample type RNA
 
Channel 1
Source name reference RNA
Organism Homo sapiens
Characteristics reference: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PC 157N2
Organism Homo sapiens
Characteristics individual: PC 157N
disease state: Normal
tissue: prostate
Growth protocol All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81248.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 21, 2012
Last update date Aug 23, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL15971
Series (1)
GSE40272 Gene-expression profiling of prostate tumors

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 35355 31111 92 109 35262 31002 42769 33450 96 122 42677 33341 40 0 15857 13855 31 68 100 100 100 100 66264 76018 1.137 .879 .781 1.009 .831 4.359 80 421 .843 .94 100 1780 6920 31 41 13 23 -100 31825 112 31714 .899 34218 34106 1.112 .799 -.153 -.323
2 23156 18744 104 122 23052 18621 24301 19330 108 134 24197 19208 5 0 15632 11574 42 70 100 98 96 95 41673 43405 1.238 .808 .794 .922 .772 6.295 80 311 .75 .94 100 1930 6910 30 40 28 38 0 19174 125 19048 .826 19774 19649 1.21 .812 -.275 -.3
3 34174 33862 111 124 34063 33737 41312 35854 132 138 41201 35729 42 0 15627 14873 85 77 100 100 98 100 67800 76930 1.01 .99 .867 1.099 1.009 3.666 80 383 .956 .96 100 2080 6890 28 38 43 53 -100 34639 127 34511 1.013 36677 36549 .987 .887 .019 -.173
4 30873 22288 106 131 30767 22156 31754 23355 132 145 31648 23223 0 0 8877 7066 90 99 100 100 100 100 52923 54871 1.389 .72 .734 .708 .729 3.527 80 367 .712 .95 110 2240 6920 30 41 58 69 0 22800 134 22665 .737 23891 23756 1.357 .751 -.441 -.414
5 2108 478 92 115 2015 363 2236 480 99 136 2143 364 0 0 621 210 45 101 100 88 100 78 2378 2507 5.551 .18 .17 .155 .182 4.489 80 308 .161 .73 110 2390 6920 30 41 73 84 0 489 118 371 .184 491 372 5.426 .174 -2.44 -2.525
6 96 120 89 112 7 8 93 102 96 123 3 -9 0 0 30 68 32 64 18 17 5 5 15 -6 .875 1.143 null 2.477 2.577 7.043 120 336 2.178 .18 120 2540 6920 30 42 88 100 -50 123 115 8 1.169 104 -9 .855 null .225 null
7 693 474 116 134 577 339 741 450 128 153 625 315 0 0 224 182 66 84 95 92 93 82 916 940 1.702 .588 .504 .554 .579 4.23 80 247 .536 .78 100 2690 6920 31 41 104 114 0 485 137 347 .601 460 322 1.664 .516 -.735 -.956
8 40627 37789 130 138 40496 37650 46682 41713 138 158 46552 41574 75 0 13852 13250 60 88 100 100 100 100 78146 88126 1.076 .93 .893 1.004 .935 3.712 80 287 .906 .95 100 2850 6910 30 40 120 130 -100 38656 141 38514 .951 42670 42528 1.051 .914 -.072 -.13
9 809 1030 105 122 703 908 818 1040 110 134 713 918 0 0 288 367 37 71 93 97 93 95 1611 1631 .774 1.292 1.288 1.271 1.27 3.982 80 289 1.222 .87 110 2990 6920 30 41 133 144 0 1054 125 929 1.321 1064 939 .757 1.317 .402 .397
10 749 749 104 115 644 634 736 741 106 129 631 626 0 0 173 230 34 70 100 100 100 98 1278 1257 1.016 .984 .992 .948 .937 3.127 80 317 .912 .86 110 3140 6910 29 40 148 159 0 766 118 649 1.007 758 640 .993 1.015 .01 .021
11 2440 2841 94 109 2345 2731 2838 3197 101 123 2743 3088 0 0 1453 1641 33 68 95 95 90 91 5076 5831 .859 1.165 1.126 1.249 1.18 4.425 120 373 1.111 .94 120 3290 6910 29 41 163 175 0 2906 112 2794 1.191 3270 3159 .839 1.152 .253 .204
12 2459 7410 89 112 2369 7298 2446 7106 96 126 2357 6993 0 0 583 2107 37 68 100 100 100 100 9667 9350 .325 3.081 2.967 3.074 2.904 2.857 80 303 3.297 .9 110 3440 6910 29 40 178 189 0 7580 115 7466 3.151 7269 7154 .317 3.035 1.656 1.602
13 1816 1173 91 115 1725 1058 1779 1205 94 124 1688 1090 0 0 442 408 32 64 100 100 100 97 2783 2778 1.63 .613 .646 .572 .601 3.38 80 327 .6 .91 110 3600 6910 29 40 194 205 0 1200 118 1082 .627 1233 1115 1.594 .661 -.673 -.598
14 653 756 94 103 559 652 654 751 99 117 560 647 0 0 131 217 34 63 100 100 100 100 1211 1207 .857 1.166 1.155 1.124 1.162 3.049 80 333 1.191 .87 110 3750 6910 29 40 209 220 0 773 105 667 1.193 768 662 .838 1.182 .255 .241
15 210 179 104 105 106 74 154 136 108 116 50 30 0 0 121 147 38 63 58 41 41 16 180 80 1.432 .698 .6 1.622 1.784 4.381 12 103 .795 .37 50 3880 6860 27 32 225 230 0 183 107 76 .714 139 31 1.4 .614 -.486 -.704
16 4947 5535 91 112 4856 5423 5284 5491 94 119 5193 5379 0 0 1927 1792 32 64 98 98 98 98 10279 10572 .895 1.117 1.036 1.257 1.093 3.693 80 354 1.051 .95 110 4050 6910 29 40 239 250 0 5662 115 5547 1.142 5617 5502 .875 1.06 .192 .084
17 371 433 87 102 284 331 374 435 89 117 287 332 0 0 93 137 29 67 98 98 98 92 615 619 .858 1.165 1.157 1.137 1.145 3.28 80 257 1.031 .74 110 4200 6900 28 39 254 265 0 443 104 339 1.192 445 340 .839 1.183 .254 .243
18 108 96 99 112 9 -15 107 78 104 127 8 -33 0 0 31 61 42 70 15 10 1 2 -6 -25 null null null 2.641 2.395 6.47 120 347 .852 .14 120 4350 6900 28 40 269 281 -50 98 115 -15 null 80 -34 null null null null
19 2667 2736 106 138 2560 2597 2606 2700 116 148 2499 2562 0 0 698 760 52 78 100 100 100 100 5157 5061 .986 1.014 1.025 1.006 1.035 2.482 80 314 .941 .92 110 4500 6900 28 39 284 295 0 2799 141 2657 1.038 2762 2621 .964 1.049 .053 .069
20 12903 32771 104 140 12799 32630 13105 31839 118 153 13000 31698 0 0 2553 6308 74 89 100 100 100 100 45429 44698 .392 2.549 2.438 2.557 2.527 2.355 80 320 2.504 .94 110 4650 6900 28 39 299 310 0 33523 143 33379 2.608 32570 32426 .383 2.494 1.383 1.319

Total number of rows: 44544

Table truncated, full table size 9901 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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